a) Field of the Invention
This invention relates to novel nucleic acid probes each of which is labeled with a fluorescent dye and/or a quencher substance. Specifically, a single-stranded oligonucleotide is labeled with the fluorescent dye and/or the quencher substance such that the intensity of fluorescence in a hybridization reaction system increases or decreases when the nucleic acid probe is hybridized with a target nucleic acid. This invention also relates to a method for determining a concentration of a nucleic acid by using the nucleic acid probe. The present invention is also concerned with determination kits, determination devices, and various measurement systems associated with such kits or devices. The present invention also pertains to a method for analyzing the kinds and amounts of various nucleic acids, a method for analyzing data obtained by such methods, and computer-readable recording media with procedures, which are required to have steps of the analysis method performed by a computer, recorded as a program.
b) Description of the Related Art
A variety of methods are conventionally known to determine a concentration of a nucleic acid by using a nucleic acid probe labeled with a fluorescent dye. These methods include:
(1) Dot blotting assay
After a target nucleic acid and a nucleic acid probe labeled with a fluorescent dye are hybridized on a membrane, unreacted nucleic probe is washed off. The intensity of fluorescence only from fluorescent dye molecules, by which the nucleic acid probe hybridized with the target nucleic acid is labeled, is measured.
(2) Method making use of an intercalator: Glazer et al., Nature, 359, 959, 1992
A certain specific fluorescent dye called “intercalator” emits strong fluorescence upon its insertion into a double strand of a nucleic acid. This method measures an increase in fluorescence from the fluorescent dye. Examples of the fluorescent dye can include ethidium bromide [Jikken Igaku (Laboratory Medicine), 15(7), 46-51, Yodosha (1997)] and SYBR R Green I (LightCycler™ System, Apr. 5, 1999; pamphlet distributed by Roche Diagnostics, Mannheim, Germany).
(3) Method making use of FRET (fluorescence energy transfer): Mergny et al., Nucleic Acid Res., 22, 920-928, 1994
This method comprises hybridizing two nucleic acid probes to a target nucleic acid. These two nucleic acid probes are labeled by different fluorescent dyes, respectively. The fluorescent dye of one of the two probes can transfer energy to the fluorescent dye or the other probe such that the latter fluorescent dye is caused to emit fluorescence. These two probes are designed such that they hybridize with their fluorescent dyes being located opposite each other and apart from each other by 1 to 9 bases. When these two nucleic acid probes hybridize to the target nucleic acid, emission of fluorescence from the latter fluorescent dye takes place. The intensity of this fluorescence emission is proportional to the number of replications of the target nucleic acid.
(4) Molecular beacon method: Tyagi et al., Nature Biotech., 14, 303-308, 1996
A nucleic acid probe for use in this method is labeled at an end thereof with a reporter dye and at an opposite end thereof with a quencher dye. As both end portions of the probe are complementary with each other in their base sequences, the overall base sequence of the probe is designed to form a hairpin stem. Owing to this structure, emission from the reporter dye is suppressed by the quencher dye under Forster resonant energy in a state suspended in a liquid. When the probe hybridizes to a target nucleic acid, the hairpin stem structure is broken. This leads to an increase in the distance between the reporter pigment and the quencher pigment, so that the transfer of Forster resonant energy no longer takes place. This allows the reporter dye to make emission.
(5) Davis's method: Davis et al., Nucleic Acids Res., 24, 702-706, 1996
This method uses DNA constructs containing one or two fluorescein molecules in flow cytometry. The fluorescein molecules were attached to the 3′ end of a DNA probe through an 18-atom spacer arm that resulted in a 10-fold increase in fluorescence intensity compared to the DNA probe to which fluorescein was directly attached to the 3′ end of the probe.
Applied to various determination methods for nucleic acids, Fish methods (fluorescent in situ hybridization assays), PCR methods, LCR methods (ligase chain reactions), SD methods (strand displacement assays), competitive hybridization and the like, significant developments have been made on these methods.
(6) Substantial technical improvements have been made on methods for amplifying a target gene by PCR [Tanpakushitsu, Kakusan, Koso (Proteins, Nucleic Acids, Enzymes), 35(17), KYORITSU SHUPPAN CO., LTD. (1990)] and conducting a polymorphous analysis on the target gene so amplified, and these polymorphous analysis methods have now found wide-spread utility in various fields such as medical field [Jikken Igaku (Laboratory Medicine), 15(7), Yodosha (1997)]. Various diseases, especially immune-related diseases have hence been elucidated from genes, thereby obtaining certain successful outcomes.
Although these methods are now widely used, they include a disadvantageous step that, subsequent to hybridization reaction between a nucleic acid probe labeled with a fluorescent dye and a target nucleic acid, an unhybridized portion of the nucleic acid probe has to be washed out of the reaction system. Obviation of this step can apparently bring about shorter determination time, simplified determination, and accurate determination. There is, accordingly, a long-standing desire for the development of a nucleic acid determination method which does not include such a step.